2OTD

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of the glycerophosphodiester phosphodiesterase from Shigella flexneri 2a

Zhang, R.Wu, R.Clancy, S.Jiang, S.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerophosphodiester phosphodiesterase
A, B, C, D
247Shigella flexneriGene Names: ugpQ
Find proteins for Q83PU8 (Shigella flexneri)
Go to UniProtKB:  Q83PU8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 80.617α = 90.00
b = 82.185β = 90.00
c = 223.202γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
SBC-Collectdata collection
HKL-3000data scaling
HKL-3000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance